It is known that auxin induces rapid gene expression changes throughout plant development, but how these transcriptional responses relate to changes in protein abundance is not well characterized. This report identifies early auxin responsive proteins in whole Arabidopsis seedlings using an iTRAQ (isobaric Tags for Relative and Absolute Quantification)-based quantitative proteomics approach. Approximately 25% of the detected proteins (1045 out of 4257 proteins) were auxin responsive, which is in line with the central role of auxin in the regulation of plant growth and development. Several well-known auxin pathway proteins were identified as differentially expressed, validating this quantitative proteomics approach. Additionally, functional categorization of these auxin responsive proteins indicates that rapid and complex metabolic changes occur in seedlings in response to auxin, including lipid metabolism. Altogether, these data describe novel auxin-regulated proteins and are an excellent resource for identifying new downstream signaling components related to auxin-mediated plant growth and development.